The Triskelion was partially, but significantly, destroyed by the Liberators when its super-soldiers pushed and scuttled S.H.I.E.L.D. Helicarriers onto the facility, which the Scarlet Witch, who was present in Nick Fury's office, used her powers in saving only the first three floors of the building and everyone within them.

While in the process of repair, the Triskelion later experienced a massive prison break caused by the Green Goblin.

During Ultimatum, the Triskelion was attacked by suicide-bomber duplicates of Jimmy Madrox until Hank Pym sacrificed himself in stopping the Madrox clones. Shortly following the events of Ultimatum, the Triskelion was undergoing another stage of repairs and became the headquarters of the Ultimates' replacements, the Avengers.

During the Avengers' tenure, the Triskelion was attacked by vampires, in which the subsequent battle resulted with the entire facility being teleported to the middle of a desert in Iran. The presence of the Triskelion caused some vocal concerns from the Iranian government, in which S.H.I.E.L.D. temporarily relocated their HQ to Stark Industries, and, with help from the European Defense Initiative, trying to find a way to return the Triskelion back to New York.

This Triskelion was finally left to the new Iranian government, pro-American, after powered rebels had taken down the former rulers, as the way to threaten Russia, China and the Arabic nations authorities.

A new Triskelion was built in New York, and in other countries, such as ones in Bangkok and SEAR.